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- PDB-5yiw: Caulobacter crescentus GcrA DNA-binding domain (DBD) in complex w... -

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Basic information

Entry
Database: PDB / ID: 5yiw
TitleCaulobacter crescentus GcrA DNA-binding domain (DBD) in complex with methylated dsDNA (crystal form 2)
Components
  • Cell cycle regulatory protein GcrA
  • DNA (5'-D(*CP*CP*CP*TP*GP*(6MA)P*TP*TP*CP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*GP*(6MA)P*AP*TP*CP*AP*GP*G)-3')
KeywordsDNA BINDING PROTEIN/DNA / Caulobacter crescentus / GcrA / DNA-binding / transcription factor / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homologyGcrA cell cycle regulator / GcrA cell cycle regulator / metal ion binding / (R,R)-2,3-BUTANEDIOL / DNA / DNA (> 10) / Cell cycle regulatory protein GcrA
Function and homology information
Biological speciesCaulobacter crescentus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.551 Å
AuthorsWu, X. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670067 China
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural insights into the unique mechanism of transcription activation by Caulobacter crescentus GcrA.
Authors: Wu, X. / Haakonsen, D.L. / Sanderlin, A.G. / Liu, Y.J. / Shen, L. / Zhuang, N. / Laub, M.T. / Zhang, Y.
History
DepositionOct 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell cycle regulatory protein GcrA
B: Cell cycle regulatory protein GcrA
C: Cell cycle regulatory protein GcrA
D: DNA (5'-D(*CP*CP*CP*TP*GP*(6MA)P*TP*TP*CP*GP*C)-3')
E: DNA (5'-D(P*GP*CP*GP*(6MA)P*AP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7386
Polymers22,6485
Non-polymers901
Water2,144119
1
A: Cell cycle regulatory protein GcrA
D: DNA (5'-D(*CP*CP*CP*TP*GP*(6MA)P*TP*TP*CP*GP*C)-3')
E: DNA (5'-D(P*GP*CP*GP*(6MA)P*AP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1044
Polymers12,0143
Non-polymers901
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-4 kcal/mol
Surface area5500 Å2
MethodPISA
2
B: Cell cycle regulatory protein GcrA


Theoretical massNumber of molelcules
Total (without water)5,3171
Polymers5,3171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3060 Å2
MethodPISA
3
C: Cell cycle regulatory protein GcrA


Theoretical massNumber of molelcules
Total (without water)5,3171
Polymers5,3171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.810, 63.658, 126.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein/peptide Cell cycle regulatory protein GcrA


Mass: 5317.199 Da / Num. of mol.: 3 / Fragment: DNA-binding domain (DBD)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (strain NA1000 / CB15N) (bacteria)
Strain: NA1000 / CB15N / Gene: gcrA, CCNA_02328 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3C9J4
#2: DNA chain DNA (5'-D(*CP*CP*CP*TP*GP*(6MA)P*TP*TP*CP*GP*C)-3')


Mass: 3299.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*CP*GP*(6MA)P*AP*TP*CP*AP*GP*G)-3')


Mass: 3397.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 8000, 0.05M Potassium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 29530 / % possible obs: 99.6 % / Redundancy: 7.2 % / Biso Wilson estimate: 19.46 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.03 / Rrim(I) all: 0.07 / Rsym value: 0.07 / Χ2: 0.95 / Net I/σ(I): 22.5
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1394 / CC1/2: 0.88 / Rpim(I) all: 0.3 / Rrim(I) all: 0.8 / Rsym value: 0.74 / Χ2: 0.95 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YIU

5yiu


Resolution: 1.551→28.745 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.68
RfactorNum. reflection% reflection
Rfree0.234 1472 5 %
Rwork0.2036 --
obs0.2052 29459 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.7 Å2
Refinement stepCycle: LAST / Resolution: 1.551→28.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1024 434 0 119 1577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061527
X-RAY DIFFRACTIONf_angle_d1.0082148
X-RAY DIFFRACTIONf_dihedral_angle_d20.786569
X-RAY DIFFRACTIONf_chiral_restr0.037253
X-RAY DIFFRACTIONf_plane_restr0.004191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5507-1.60070.32941260.26952488X-RAY DIFFRACTION99
1.6007-1.6580.27921310.24142510X-RAY DIFFRACTION100
1.658-1.72430.28751220.21662508X-RAY DIFFRACTION99
1.7243-1.80280.22231390.20432524X-RAY DIFFRACTION100
1.8028-1.89780.26191330.20872537X-RAY DIFFRACTION100
1.8978-2.01670.23731270.21432575X-RAY DIFFRACTION100
2.0167-2.17240.27061280.20172520X-RAY DIFFRACTION100
2.1724-2.39090.21521430.20392568X-RAY DIFFRACTION100
2.3909-2.73660.23271370.22322562X-RAY DIFFRACTION100
2.7366-3.44690.2511320.21532570X-RAY DIFFRACTION99
3.4469-28.75040.20811540.17842625X-RAY DIFFRACTION97

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